data_A1EDD # _chem_comp.id A1EDD _chem_comp.name N-METHYLSULFONYL-D-LYSINE _chem_comp.type "D-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C7 H16 N2 O4 S" _chem_comp.mon_nstd_parent_comp_id DLY _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-10-12 _chem_comp.pdbx_modified_date 2026-01-02 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 224.278 _chem_comp.one_letter_code K _chem_comp.three_letter_code A1EDD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 9JW9 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm Y # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal A1EDD N N1 N 0 1 N N N Y Y N 75.312 -19.811 3.991 0.868 -0.239 -0.628 N A1EDD 1 A1EDD CA C1 C 0 1 N N R N Y N 74.801 -20.444 2.766 0.395 0.866 0.209 CA A1EDD 2 A1EDD C C2 C 0 1 N N N N Y Y 73.334 -20.865 2.903 1.271 2.072 -0.009 C A1EDD 3 A1EDD O O1 O 0 1 N N N N Y Y 72.695 -21.310 1.905 2.196 2.015 -0.785 O A1EDD 4 A1EDD CB C3 C 0 1 N N N N N N 75.038 -19.519 1.543 -1.048 1.209 -0.166 CB A1EDD 5 A1EDD CG C4 C 0 1 N N N N N N 73.976 -18.429 1.348 -1.958 0.026 0.172 CG A1EDD 6 A1EDD CD C5 C 0 1 N N N N N N 74.258 -17.649 0.028 -3.401 0.369 -0.203 CD A1EDD 7 A1EDD CE C6 C 0 1 N N N N N N 73.130 -16.616 -0.248 -4.311 -0.814 0.135 CE A1EDD 8 A1EDD NZ N2 N 0 1 N N N N N N 73.294 -16.036 -1.601 -5.696 -0.484 -0.225 NZ A1EDD 9 A1EDD C25 C7 C 0 1 N N N N N N 75.372 -22.206 5.362 0.938 -2.200 1.291 C25 A1EDD 10 A1EDD O23 O2 O 0 1 N N N N N N 77.434 -20.692 4.906 2.154 -2.255 -1.084 O23 A1EDD 11 A1EDD O24 O3 O 0 1 N N N N N N 75.695 -19.847 6.410 2.951 -0.603 0.576 O24 A1EDD 12 A1EDD S22 S1 S 0 1 N N N N N N 76.042 -20.585 5.230 1.903 -1.369 -0.001 S22 A1EDD 13 A1EDD H1 H1 H 0 1 N N N N N N 75.974 -19.130 3.679 0.572 -0.311 -1.549 H1 A1EDD 14 A1EDD H2 H2 H 0 1 N N N N N N 75.385 -21.360 2.591 0.437 0.571 1.258 H2 A1EDD 15 A1EDD H4 H4 H 0 1 N N N N N N 75.057 -20.145 0.639 -1.370 2.087 0.393 H4 A1EDD 16 A1EDD H5 H5 H 0 1 N N N N N N 76.014 -19.028 1.669 -1.106 1.417 -1.235 H5 A1EDD 17 A1EDD H6 H6 H 0 1 N N N N N N 74.008 -17.732 2.198 -1.636 -0.852 -0.387 H6 A1EDD 18 A1EDD H7 H7 H 0 1 N N N N N N 72.981 -18.894 1.292 -1.900 -0.183 1.241 H7 A1EDD 19 A1EDD H8 H8 H 0 1 N N N N N N 74.309 -18.361 -0.809 -3.723 1.247 0.356 H8 A1EDD 20 A1EDD H9 H9 H 0 1 N N N N N N 75.218 -17.120 0.119 -3.459 0.578 -1.271 H9 A1EDD 21 A1EDD H10 H10 H 0 1 N N N N N N 73.181 -15.812 0.501 -3.989 -1.692 -0.424 H10 A1EDD 22 A1EDD H11 H11 H 0 1 N N N N N N 72.153 -17.117 -0.183 -4.253 -1.022 1.204 H11 A1EDD 23 A1EDD H12 H12 H 0 1 N N N N N N 72.565 -15.373 -1.771 -6.317 -1.250 -0.011 H12 A1EDD 24 A1EDD H13 H13 H 0 1 N N N N N N 74.181 -15.579 -1.662 -5.997 0.363 0.232 H13 A1EDD 25 A1EDD H15 H15 H 0 1 N N N N N N 75.857 -22.737 6.194 0.055 -2.660 0.845 H15 A1EDD 26 A1EDD H16 H16 H 0 1 N N N N N N 74.290 -22.141 5.549 1.548 -2.970 1.763 H16 A1EDD 27 A1EDD H17 H17 H 0 1 N N N N N N 75.550 -22.754 4.425 0.629 -1.471 2.039 H17 A1EDD 28 A1EDD OXT O4 O 0 1 N Y N Y Y N 72.789 -20.749 4.109 1.024 3.211 0.658 O1 A1EDD 29 A1EDD HXT H3 H 0 1 N Y N Y Y N 71.887 -21.045 4.079 1.613 3.958 0.485 H3 A1EDD 30 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A1EDD NZ CE SING N N 1 A1EDD CE CD SING N N 2 A1EDD CD CG SING N N 3 A1EDD CG CB SING N N 4 A1EDD CB CA SING N N 5 A1EDD O C DOUB N N 6 A1EDD CA C SING N N 7 A1EDD CA N SING N N 8 A1EDD N S22 SING N N 9 A1EDD O23 S22 DOUB N N 10 A1EDD S22 C25 SING N N 11 A1EDD S22 O24 DOUB N N 12 A1EDD N H1 SING N N 13 A1EDD CA H2 SING N N 14 A1EDD CB H4 SING N N 15 A1EDD CB H5 SING N N 16 A1EDD CG H6 SING N N 17 A1EDD CG H7 SING N N 18 A1EDD CD H8 SING N N 19 A1EDD CD H9 SING N N 20 A1EDD CE H10 SING N N 21 A1EDD CE H11 SING N N 22 A1EDD NZ H12 SING N N 23 A1EDD NZ H13 SING N N 24 A1EDD C25 H15 SING N N 25 A1EDD C25 H16 SING N N 26 A1EDD C25 H17 SING N N 27 A1EDD C OXT SING N N 28 A1EDD OXT HXT SING N N 29 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor A1EDD InChI InChI 1.06 "InChI=1S/C7H16N2O4S/c1-14(12,13)9-6(7(10)11)4-2-3-5-8/h6,9H,2-5,8H2,1H3,(H,10,11)/t6-/m1/s1" A1EDD InChIKey InChI 1.06 DMTLUNPNQAZANT-ZCFIWIBFSA-N A1EDD SMILES_CANONICAL CACTVS 3.385 "C[S](=O)(=O)N[C@H](CCCCN)C(O)=O" A1EDD SMILES CACTVS 3.385 "C[S](=O)(=O)N[CH](CCCCN)C(O)=O" A1EDD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CS(=O)(=O)N[C@H](CCCCN)C(=O)O" A1EDD SMILES "OpenEye OEToolkits" 2.0.7 "CS(=O)(=O)NC(CCCCN)C(=O)O" # _pdbx_chem_comp_identifier.comp_id A1EDD _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(2~{R})-6-azanyl-2-(methylsulfonylamino)hexanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1EDD "Create component" 2024-10-12 PDBC A1EDD "Modify coordinates" 2024-10-17 PDBC A1EDD "Initial release" 2026-01-07 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1EDD _pdbx_chem_comp_pcm.modified_residue_id DLY _pdbx_chem_comp_pcm.type Methylsulfanylation _pdbx_chem_comp_pcm.category "Named protein modification" _pdbx_chem_comp_pcm.position "Amino-acid backbone" _pdbx_chem_comp_pcm.polypeptide_position N-terminal _pdbx_chem_comp_pcm.comp_id_linking_atom ? _pdbx_chem_comp_pcm.modified_residue_id_linking_atom ? _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #